Variant report

Variant	rs2414426
Chromosome Location	chr15:56005732-56005733
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56002955..56005054-chr15:56005105..56008036,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10518817	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[AMR][1000 genomes]
rs10851589	0.80[CEU][hapmap];0.95[CHB][hapmap]
rs10851591	0.89[ASN][1000 genomes]
rs11630141	0.87[ASN][1000 genomes]
rs11854213	0.86[CHB][hapmap]
rs12373006	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12438177	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs12442771	0.86[CHB][hapmap]
rs12591246	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592192	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12594642	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12903822	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.81[ASN][1000 genomes]
rs1371056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1530087	0.80[CEU][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1550330	0.85[AMR][1000 genomes]
rs16976450	0.81[CHB][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes]
rs16976472	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1814329	0.86[CHB][hapmap]
rs2008336	0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2118781	0.86[CHB][hapmap]
rs2414424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2414427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2414431	0.82[CHB][hapmap]
rs28485308	0.82[ASN][1000 genomes]
rs28575567	0.81[ASN][1000 genomes]
rs4377101	0.82[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4774220	0.81[ASN][1000 genomes]
rs4774800	0.86[CHB][hapmap]
rs4774802	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4774803	0.88[ASN][1000 genomes]
rs572531	0.95[MEX][hapmap];0.83[AMR][1000 genomes]
rs62043869	0.90[AMR][1000 genomes]
rs62043871	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62043872	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493805	0.86[AMR][1000 genomes]
rs6493809	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs6493814	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs71110312	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs715321	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7161967	0.82[ASN][1000 genomes]
rs7162371	0.89[ASN][1000 genomes]
rs7162879	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7163167	0.85[CHB][hapmap]
rs7171318	0.95[CHB][hapmap]
rs7178379	0.95[CHB][hapmap]
rs7180112	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7181212	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs7182733	0.86[CHB][hapmap]
rs7359255	0.86[CHB][hapmap]
rs8023911	0.81[ASN][1000 genomes]
rs8025445	0.86[CHB][hapmap]
rs8031192	0.86[AMR][1000 genomes]
rs8034113	0.83[AMR][1000 genomes]
rs8034414	0.87[ASN][1000 genomes]
rs8037136	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs8042029	0.84[ASN][1000 genomes]
rs9920076	0.80[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes]
rs9920246	0.91[CHB][hapmap]
rs9920262	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2414426	CCPG1	cis	parietal	SCAN
rs2414426	MYO5C	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55996200-56015000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:55996400-56007600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:55999800-56028000	Weak transcription	Fetal Kidney	kidney
4	chr15:56001000-56007600	Weak transcription	Hela-S3	cervix
5	chr15:56001200-56007600	Weak transcription	HepG2	liver
6	chr15:56002200-56007400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:56002200-56014600	Weak transcription	A549	lung
8	chr15:56003400-56011400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:56003800-56008000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:56004000-56007800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:56004000-56008200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:56004000-56012800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:56004400-56011000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:56005400-56005800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr15:56005600-56005800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr15:56005600-56006200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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